Viruses called bacteriophages can infect and set in motion a genetic takeover of bacteria, such as Escherichia coli Bacteria are prokaryotes with cells.

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Presentation on theme: "Viruses called bacteriophages can infect and set in motion a genetic takeover of bacteria, such as Escherichia coli Bacteria are prokaryotes with cells."— Presentation transcript:

1Viruses called bacteriophages can infect and set in motion a genetic takeover of bacteria, such as Escherichia coliBacteria are prokaryotes with cells much smaller and more simply organized than those of eukaryotesViruses are smaller and simpler than bacteria

2Tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic colorationIn the late 1800s, researchers hypothesized that a particle smaller than bacteria caused the diseaseIn 1935, Wendell Stanley confirmed this hypothesis by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV)

3Viral genomes may consist ofViruses are not cellsViruses are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelopeViral genomes may consist ofDouble- or single-stranded DNADouble- or single-stranded RNADepending on its type of nucleic acid, a virus is called a DNA virus or an RNA virus

4Capsomereof capsidRNA18  250 mmTobacco mosaic virus20 nmA capsid is the protein shell that encloses the viral genome and can have various structures

6Some viruses have structures that have membranous envelopes that help them infect hostsThese viral envelopes surround the capsids of influenza viruses and many other viruses found in animalsViral envelopes, which are derived from the host cell’s membrane, contain a combination of viral and host cell molecules

8Bacteriophages, also called phages, are viruses that infect bacteriaPhages have an elongated capsid head that encloses their DNAA protein tailpiece attaches the phage to the host and injects the phage DNA insideViruses use enzymes, ribosomes, and small host molecules to synthesize progeny viruses

11The Lytic CycleThe lytic cycle is a phage reproductive cycle that culminates in the death of the host cellThe lytic cycle produces new phages and digests the host’s cell wall, releasing the progeny virusesA phage that reproduces only by the lytic cycle is called a virulent phageBacteria have defenses against phages, including restriction enzymes that recognize and cut up certain phage DNA

13The Lysogenic CycleThe lysogenic cycle replicates the phage genome without destroying the hostThe viral DNA molecule is incorporated by genetic recombination into the host cell’s chromosomeThis integrated viral DNA is known as a prophageEvery time the host divides, it copies the phage DNA and passes the copies to daughter cellsPhages that use both the lytic and lysogenic cycles are called temperate phages

15Reproductive Cycles of Animal VirusesTwo key variables in classifying viruses that infect animals:DNA or RNA?Single-stranded or double-stranded?Viral EnvelopesMany viruses that infect animals have a membranous envelopeViral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell

17RNA as Viral Genetic MaterialThe broadest variety of RNA genomes is found in viruses that infect animalsRetroviruses use reverse transcriptase to copy their RNA genome into DNAHIV is the retrovirus that causes AIDS

19The viral DNA that is integrated into the host genome is called a provirusUnlike a prophage, a provirus remains a permanent resident of the host cellThe host’s RNA polymerase transcribes the proviral DNA into RNA moleculesThe RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new virus particles released from the cell

21Viroids and Prions: The Simplest Infectious AgentsViroids are circular RNA molecules that infect plants and disrupt their growthPrions are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammalsPrions propagate by converting normal proteins into the prion version

23The Bacterial Genome and Its ReplicationThe bacterial chromosome is usually a circular DNA molecule with few associated proteinsMany bacteria also have plasmids, smaller circular DNA molecules that can replicate independently of the chromosomeBacterial cells divide by binary fission, which is preceded by replication of the chromosome

24Mutation and Genetic Recombination as Sources of Genetic VariationSince bacteria can reproduce rapidly, new mutations quickly increase genetic diversityMore genetic diversity arises by recombination of DNA from two different bacterial cellsThree processes bring bacterial DNA from different individuals together:TransformationTransductionConjugation

25Transformation and TransductionTransformation is the alteration of a bacterial cell’s genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environmentFor example, harmless Streptococcus pneumoniae bacteria can be transformed to pneumonia-causing cellsIn the process known as transduction, phages carry bacterial genes from one host cell to another

27Conjugation and PlasmidsConjugation is the direct transfer of genetic material between bacterial cells that are temporarily joinedThe transfer is one-way: One cell (“male”) donates DNA, and its “mate” (“female”) receives the genes

30The F Plasmid and ConjugationCells containing the F plasmid, designated F+ cells (fertile), function as DNA donors during conjugationF+ cells transfer DNA to an F recipient cellChromosomal genes can be transferred during conjugation when the donor cell’s F factor is integrated into the chromosomeA cell with a built-in F factor is called an Hfr cellThe F factor of an Hfr (high frequency of recombination) cell brings some chromosomal DNA along when transferred to an F– cell

31F plasmidBacterial chromosomeF+ cellF+ cellMatingbridgeF– cellF+ cellBacterialchromosomeConjunction and transfer of an F plasmid from and F+ donor to an F– recipientF+ cellHfr cellF factorHfr cellF– cellTemporarypartialdiploidRecombinant F–bacteriumConjugation and transfer of part of the bacterial chromosome from anHfr donor to an F– recipient, resulting in recombination

32R plasmids and Antibiotic ResistanceR plasmids confer resistance to various antibioticsWhen a bacterial population is exposed to an antibiotic, individuals with the R plasmid will survive and increase in the overall populationTransposition of Genetic ElementsThe DNA of a cell can also undergo recombination due to movement of transposable elements within the cell’s genomeTransposable elements, often called “jumping genes,” contribute to genetic shuffling in bacteria

33Insertion SequencesThe simplest transposable elements, called insertion sequences, exist only in bacteriaAn insertion sequence has a single gene for transposase, an enzyme catalyzing movement of the insertion sequence from one site to another within the genome

35TransposonsTransposable elements called transposons are longer and more complex than insertion sequencesIn addition to DNA required for transposition, transposons have extra genes that “go along for the ride,” such as genes for antibiotic resistance

37Operons: The Basic ConceptIn bacteria, genes are often clustered into operons, composed ofAn operator, an “on-off” switchA promoterGenes for metabolic enzymesAn operon can be switched off by a protein called a repressorA corepressor is a small molecule that cooperates with a repressor to switch an operon off

38Polypeptides that make up enzymes for tryptophan synthesistrp operonPromoterPromoterGenes of operonDNAtrpRtrpEtrpDtrpCtrpBtrpAOperatorRegulatorygeneRNApolymeraseStart codonStop codon3¢mRNA 5¢mRNA5¢EDCBAProteinInactiverepressorPolypeptides that make upenzymes for tryptophan synthesisTryptophan absent, repressor inactive, operon on

41Repressible and Inducible Operons: Two Types of Negative Gene RegulationA repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcriptionThe trp operon is a repressible operonAn inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcriptionThe classic example of an inducible operon is the lac operon, which contains genes coding for enzymes in hydrolysis and metabolism of lactose

44Inducible enzymes usually function in catabolic pathwaysRepressible enzymes usually function in anabolic pathwaysRegulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor

45Positive Gene RegulationSome operons are also subject to positive control through a stimulatory activator protein, such as catabolite activator protein (CAP)When glucose (a preferred food source of E.coli ) is scarce, the lac operon is activated by the binding of CAPWhen glucose levels increase, CAP detaches from the lac operon, turning it off

48Two features of eukaryotic genomes are a major information-processing challenge:First, the typical eukaryotic genome is much larger than that of a prokaryotic cellSecond, cell specialization limits the expression of many genes to specific cellsThe DNA-protein complex, called chromatin, is ordered into higher structural levels than the DNA-protein complex in prokaryotes

49Nucleosomes, or “Beads on a String”Proteins called histones are responsible for the first level of DNA packing in chromatinThe association of DNA and histones seems to remain intact throughout the cell cycleIn electron micrographs, unfolded chromatin has the appearance of beads on a stringEach “bead” is a nucleosome, the basic unit of DNA packing

54Differential Gene ExpressionDifferences between cell types result from differential gene expression, the expression of different genes by cells within the same genomeIn each type of differentiated cell, a unique subset of genes is expressedMany key stages of gene expression can be regulated in eukaryotic cells

56Regulation of Chromatin StructureGenes within highly packed heterochromatin are usually not expressedChemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression

59DNA MethylationDNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some speciesIn some species, DNA methylation causes long-term inactivation of genes in cellular differentiationIn genomic imprinting, methylation turns off either the maternal or paternal alleles of certain genes at the start of development … lions, tigers, ligers?

60The Roles of Transcription FactorsTo initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factorsGeneral transcription factors are essential for the transcription of all protein-coding genesIn eukaryotes, high levels of transcription of particular genes depend on control elements interacting with specific transcription factors

61Enhancers and Specific Transcription FactorsProximal control elements are located close to the promoterDistal control elements, groups of which are called enhancers, may be far away from a gene or even in an intronAn activator is a protein that binds to an enhancer and stimulates transcription of a gene

65In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as intronsExonsDNAPrimaryRNAtranscriptRNA splicingormRNA

66mRNA DegradationThe life span of mRNA molecules in the cytoplasm is a key to determining the protein synthesisThe mRNA life span is determined in part by sequences in the leader and trailer regionsRNA interference by single-stranded microRNAs (miRNAs) can lead to degradation of an mRNA or block its translationThe phenomenon of inhibition of gene expression by RNA molecules is called RNA interference (RNAi)

67ProteincomplexDegradation of mRNADicerORmiRNATarget mRNAHydrogenbondBlockage of translation

68Protein Processing and DegradationAfter translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to controlProteasomes are giant protein complexes that bind protein molecules and degrade them

70Types of Genes Associated with CancerGenes that normally regulate cell growth and division during the cell cycle include:Genes for growth factorsTheir receptorsIntracellular molecules of signaling pathwaysMutations altering any of these genes in somatic cells can lead to cancer

71Oncogenes and Proto-OncogenesOncogenes are cancer-causing genesProto-oncogenes are normal cellular genes that code for proteins that stimulate normal cell growth and divisionA DNA change that makes a proto-oncogene excessively active converts it to an oncogene, which may promote excessive cell division and cancer

72Proto-oncogeneDNAPoint mutationwithin a controlelementTranslocation or transposition:gene moved to new locus,under new controlsPoint mutationwithin the geneGene amplification:multiple copies of the geneNewpromoterOncogeneOncogeneNormal growth-stimulatingprotein in excessNormal growth-stimulatingprotein in excessNormal growth-stimulatingprotein in excessHyperactive ordegradation-resistant protein

74Interference with Normal Cell-Signaling PathwaysMany proto-oncogenes and tumor suppressor genes encode components of growth-stimulating and growth-inhibiting pathways, respectivelyThe Ras protein, encoded by the ras gene, is a G protein that relays a signal from a growth factor receptor to a cascade of protein kinasesMany ras oncogenes have a mutation that leads to a hyperactive Ras protein that issues signals on its own, resulting in excessive cell division

75The p53 gene,“guardian angel of the genome” encodes a tumor-suppressor protein that is a specific transcription factor that promotes synthesis of cell cycle–inhibiting proteinsMutations that knock out the p53 gene can lead to excessive cell growth and cancerIncreased cell division, possibly leading to cancer, can result if the cell cycle is over stimulated or not inhibited when it normally would be

78Transposable Elements and Related SequencesThe first evidence for wandering DNA segments came from geneticist Barbara McClintock’s breeding experiments with Indian cornMcClintock identified changes in the color of corn kernels that made sense only by postulating that some genetic elements move from other genome locations into the genes for kernel color

80Movement of Transposons and RetrotransposonsEukaryotic transposable elements are of two types:Transposons, which move within a genome by means of a DNA intermediateRetrotransposons, which move by means of an RNA intermediate

82Genes and Multigene FamiliesMost eukaryotic genes are present in one copy per haploid set of chromosomesThe rest of the genome occurs in multigene families, collections of identical or very similar genesGlobin gene family clusters also include pseudogenes, nonfunctional nucleotide sequences that are similar to the functional genes

83DNARNA transcriptsNon-transcribedspacerTranscription unitDNA18S5.8S28SrRNA5.8S28S18SPart of the ribosomal RNA gene family

85DNA technology has revolutionized biotechnology, the manipulation of organisms or their genetic components to make useful productsAn example of DNA technology is the microarray, a measurement of gene expression of thousands of different genes

86DNA Cloning and Its ApplicationsTo work directly with specific genes, scientists prepare gene-sized pieces of DNA in identical copies, a process called gene cloningMost methods for cloning pieces of DNA in the laboratory share general features, such as the use of bacteria and their plasmidsCloned genes are useful for making copies of a particular gene and producing a gene product

91Amplifying DNA in Vitro: The Polymerase Chain Reaction (PCR)The polymerase chain reaction, PCR, can produce many copies of a specific target segment of DNAA three-step cycle—heating, cooling, and replication—brings about a chain reaction that produces an exponentially growing population of identical DNA molecules

93Gel ElectrophoresisOne indirect method of rapidly analyzing and comparing genomes is gel electrophoresisThis technique uses a gel as a molecular sieve to separate nuclei acids or proteins by sizeIn restriction fragment analysis, DNA fragments produced by restriction enzyme digestion of a DNA molecule are sorted by gel electrophoresisRestriction fragment analysis is useful for comparing two different DNA molecules, such as two alleles for a gene

96Medical ApplicationsOne benefit of DNA technology is identification of human genes in which mutation plays a role in genetic diseasesScientists can diagnose many human genetic disorders by using PCR and primers corresponding to cloned disease genes, then sequencing the amplified product to look for the disease-causing mutationEven when a disease gene has not been cloned, presence of an abnormal allele can be diagnosed if a closely linked RFLP marker has been found

98Human Gene TherapyGene therapy is the alteration of an afflicted individual’s genesGene therapy holds great potential for treating disorders traceable to a single defective geneVectors are used for delivery of genes into cellsGene therapy raises ethical questions, such as whether human germ-line cells should be treated to correct the defect in future generations

100Pharmaceutical ProductsSome pharmaceutical applications of DNA technology:Large-scale production of human hormones and other proteins with therapeutic usesProduction of safer vaccines

101Forensic EvidenceDNA “fingerprints” obtained by analysis of tissue or body fluids can provide evidence in criminal and paternity casesA DNA fingerprint is a specific pattern of bands of RFLP markers on a gelThe probability that two people who are not identical twins have the same DNA fingerprint is very smallExact probability depends on the number of markers and their frequency in the population

111What does the operon model attempt to explain?the coordinated control of gene expression in bacteriabacterial resistance to antibioticshow genes move between homologous regions of DNAthe mechanism of viral attachment to a host cellhorizontal transmission of plant virusesAnswer: A

112What does the operon model attempt to explain?the coordinated control of gene expression in bacteriabacterial resistance to antibioticshow genes move between homologous regions of DNAthe mechanism of viral attachment to a host cellhorizontal transmission of plant viruses112

113The repressor is active and binds to the operator. When tryptophan (an amino acid) is present in the external medium, the bacterium brings in the tryptophan and does not need to make this amino acid. Which of the following is true when there is no tryptophan in the medium?The repressor is active and binds to the operator.The repressor is inactive, and RNA polymerase moves through the operator.The operator is bound, and mRNA is made.Genes are inactive.The corepressor binds to the repressor.Answer: B113

114The repressor is active and binds to the operator. When tryptophan (an amino acid) is present in the external medium, the bacterium brings in the tryptophan and does not need to make this amino acid. Which of the following is true when there is no tryptophan in the medium?The repressor is active and binds to the operator.The repressor is inactive, and RNA polymerase moves through the operator.The operator is bound, and mRNA is made.Genes are inactive.The corepressor binds to the repressor.114

115mutation in lac (-galactosidase gene) Each of a group of bacterial cells has a mutation in its lac operon. Which of the following will make it impossible for the cell to metabolize lactose?mutation in lac (-galactosidase gene)mutation in lac (cannot bind to operator)mutation in operator (cannot bind to repressor)mutation in lac (cannot bind to inducer)Answer: AFigure 18.4115

116mutation in lac (-galactosidase gene) Each of a group of bacterial cells has a mutation in its lac operon. Which of the following will make it impossible for the cell to metabolize lactose?mutation in lac (-galactosidase gene)mutation in lac (cannot bind to operator)mutation in operator (cannot bind to repressor)mutation in lac (cannot bind to inducer)116

117Which element(s) from the following list constitute(s) a bacterial operon?repressor genepromoterinducerrepressor proteinall of the aboveAnswer: B117

118Which element(s) from the following list constitute(s) a bacterial operon?repressor genepromoterinducerrepressor proteinall of the above118

119Which of the following statements about specific transcription factors is false?The binding of specific transcription factors to the control elements of enhancers influences the rate of gene expression.Specific transcription factors include activators and repressors.MyoD is one.Some act indirectly by affecting chromatin structure.Interaction of specific transcription factors and RNA polymerase II with a promoter leads to a low rate of initiation and production of a few RNA transcripts.Answer: E119

120Which of the following statements about specific transcription factors is false?The binding of specific transcription factors to the control elements of enhancers influences the rate of gene expression.Specific transcription factors include activators and repressors.MyoD is one.Some act indirectly by affecting chromatin structure.Interaction of specific transcription factors and RNA polymerase II with a promoter leads to a low rate of initiation and production of a few RNA transcripts.120

121Approximately what proportion of the DNA in the human genome codes for proteins or functional RNA?83%46%32%13%1.5%Answer: EConcept 18.3121

122Approximately what proportion of the DNA in the human genome codes for proteins or functional RNA?83%46%32%13%1.5%122

123A specific gene is known to code for three different but related proteins. This could be due to which of the following?premature mRNA degradationalternative RNA splicinguse of different enhancersprotein degradationdifferential transportAnswer: B123

124A specific gene is known to code for three different but related proteins. This could be due to which of the following?premature mRNA degradationalternative RNA splicinguse of different enhancersprotein degradationdifferential transport124

125RNA is cut up into small 22-nucleotide fragments to regulate another “target” mRNA. Which of the following is/are true?The target mRNA is degraded, and its protein is not made.The RNA fragments enhance protein synthesis by the mRNA.The RNA fragments bind the ribosome to enhance use of the mRNA and protein synthesis.The target mRNA is blocked from being used in translation.The RNA fragments act on the ribosome to shut down translation of all mRNAs.Answer: A or DFigure 18.14125

126RNA is cut up into small 22-nucleotide fragments to regulate another “target” mRNA. Which of the following is/are true?The target mRNA is degraded, and its protein is not made.The RNA fragments enhance protein synthesis by the mRNA.The RNA fragments bind the ribosome to enhance use of the mRNA and protein synthesis.The target mRNA is blocked from being used in translation.The RNA fragments act on the ribosome to shut down translation of all mRNAs.126

127At fertilization, specific cells are destined for certain functions. Even though the two cells have numerous transcription factors and many are present in both cells, the lens cell makes the crystallin protein (not albumin), whereas the liver cell makes albumin (not crystallin). Which of the following explains this cell specificity?Specific transcription factors made in the cell determine which genes are expressed.At fertilization, specific cells are destined for certain functions.The activators needed for expression of the crystallin gene are present in all cells.The promoters are different for the different genes.Answer: ASee Figure 18.11, although different combinations of transcription factors are present.127

128At fertilization, specific cells are destined for certain functions. Even though the two cells have numerous transcription factors and many are present in both cells, the lens cell makes the crystallin protein (not albumin), whereas the liver cell makes albumin (not crystallin). Which of the following explains this cell specificity?Specific transcription factors made in the cell determine which genes are expressed.At fertilization, specific cells are destined for certain functions.The activators needed for expression of the crystallin gene are present in all cells.The promoters are different for the different genes.Answer: ASee Figure 18.11, although different combinations of transcription factors are present.128

129Differential gene expression (different genes turned on in different cells) leads to different tissues developing in the embryo. Which of the following is not a cause of differential gene expression?cytoplasmic determinantsinductionthe environment around a particular cellcorepressor proteinsAnswer: (1) Cytoplasmic determinants. Molecules that are localized within the zygote get put into different cells during cleavage of the embryo and regulate transcription, mRNA usage, or protein activity to cause differentiation of the embryonic cell. (2) Induction. A hormone (or inducer, signaling molecule) will be released by one cell of the embryo and bind to another cell to induce changes in the other cell.

130Differential gene expression (different genes turned on in different cells) leads to different tissues developing in the embryo. Which of the following is not a cause of differential gene expression?cytoplasmic determinantsinductionthe environment around a particular cellcorepressor proteinsAnswer: (1) Cytoplasmic determinants. Molecules that are localized within the zygote get put into different cells during cleavage of the embryo and regulate transcription, mRNA usage, or protein activity to cause differentiation of the embryonic cell. (2) Induction. A hormone (or inducer, signaling molecule) will be released by one cell of the embryo and bind to another cell to induce changes in the other cell.

131Initially, cytoplasmic determinants are localized in one part of a zygote and could be which of the following? (Choose more than one answer.)genemRNAtranscription factorribosomemyoblastAnswer: B, C131

132Initially, cytoplasmic determinants are localized in one part of a zygote and could be which of the following? (Choose more than one answer.)genemRNAtranscription factorribosomemyoblast132

133Anterior structures would form at both ends. Scientists showed that bicoid mRNA, and then its Bicoid protein, is normally found in highest concentrations in the fly’s anterior. What would happen if Bicoid were injected at the posterior end?Anterior structures would form at both ends.Posterior structures would form at both ends.The embryo would have no dorsal-ventral axis.Bicoid mRNA wouldn’t be translated into protein.Answer: A. Figure Anterior structures would form at both ends.133

134Anterior structures would form at both ends. Scientists showed that bicoid mRNA, and then its Bicoid protein, is normally found in highest concentrations in the fly’s anterior. What would happen if Bicoid were injected at the posterior end?Anterior structures would form at both ends.Posterior structures would form at both ends.The embryo would have no dorsal-ventral axis.Bicoid mRNA wouldn’t be translated into protein.Answer: A. Figure Anterior structures would form at both ends.134

135Mutations in _______ genes caused the development of legs in the place of antennae.homeoticembryonic lethalmyoDRaswild-typeWild typeEyeMutantAnswer: A. homeotic Figure 18.20135

136Mutations in _______ genes caused the development of legs in the place of antennae.homeoticembryonic lethalmyoDRaswild-typeWild typeEyeMutantAnswer: A. homeotic Figure 18.20136

137The shape of an organ, the number of brain cells in an embryonic brain, the removal of mutated cells, and the webbing cells between the toes of a human embryo are all regulated by which of the following?certain cells becoming much largercertain cells shrinkingcertain cells dyingformation of embryonic cellsconcentration of Bicoid proteinAnswer: C137

138The shape of an organ, the number of brain cells in an embryonic brain, the removal of mutated cells, and the webbing cells between the toes of a human embryo are all regulated by which of the following?certain cells becoming much largercertain cells shrinkingcertain cells dyingformation of embryonic cellsconcentration of Bicoid proteinAnswer: C138

139Which of the following would not typically cause a proto-oncogene to become an oncogene?gene suppressiontranslocationamplificationpoint mutationretroviral activationAnswer: A139

140Which of the following would not typically cause a proto-oncogene to become an oncogene?gene suppressiontranslocationamplificationpoint mutationretroviral activation140

141Which of the following statements about the APC gene is false?It is a tumor-suppressor gene.It is mutated in 60% of colorectal cancers.It regulates cell migration and adhesion.It may be deleted in colon cancer.Mutations in one allele are enough to lose the gene’s function.Answer: E. Figure 18.26141

142Which of the following statements about the APC gene is false?It is a tumor-suppressor gene.It is mutated in 60% of colorectal cancers.It regulates cell migration and adhesion.It may be deleted in colon cancer.Mutations in one allele are enough to lose the gene’s function.Answer: E. Figure 18.26142

143Scientific Skills ExerciseThe diagrams on the next slide show an intact DNA sequence (top) and three experimental DNA sequences. A red X indicates the possible control element (1, 2, or 3) that was deleted in each experimental DNA sequence. The area between the slashes represents the approximately 8 kilobases of DNA located between the promoter and the enhancer region. The horizontal bar graph shows the amount of reporter gene mRNA that was present in each cell culture after 48 hours relative to the amount that was in the culture containing the intact enhancer region (top bar = 100%).

145What was the independent variable in this experiment?the length of time that the cells were incubatedthe relative level of reporter gene mRNAthe distance between the promoter and the enhancerthe possible control element that was deletedAnswer: D

146What was the independent variable in this experiment?the length of time that the cells were incubatedthe relative level of reporter gene mRNAthe distance between the promoter and the enhancerthe possible control element that was deleted

147What was the dependent variable in this experiment?the length of time that the cells were incubatedhow many of the artificial DNA molecules were taken up by the cellsthe relative level of reporter gene mRNAthe distance between the promoter and the enhancerAnswer: C

148What was the dependent variable in this experiment?the length of time that the cells were incubatedhow many of the artificial DNA molecules were taken up by the cellsthe relative level of reporter gene mRNAthe distance between the promoter and the enhancerAnswer: C

149What was the control treatment in this experiment?the reporter genethe construct that had no DNA deleted from the enhancerthe temperature, pH, and salt concentration of the incubation mediumthe construct that resulted in the lowest amount of reporter mRNAAnswer: B

150What was the control treatment in this experiment?the reporter genethe construct that had no DNA deleted from the enhancerthe temperature, pH, and salt concentration of the incubation mediumthe construct that resulted in the lowest amount of reporter mRNA

151Do the data suggest that any of these possible control elements are actual control elements?Only control elements 1 and 2 appear to be control elements.Only control element 3 appears to be a control element.All three appear to be control elements.None of the possible control elements appear to be actual control elements.Answer: C

152Do the data suggest that any of these possible control elements are actual control elements?Only control elements 1 and 2 appear to be control elements.Only control element 3 appears to be a control element.All three appear to be control elements.None of the possible control elements appear to be actual control elements.Answer: C

153Did deletion of any of the possible control elements cause a reduction in reporter gene expression? How can you tell?Deletion of element 3 caused a reduction in reporter gene expression; that construct resulted in less than 50% of the control level of mRNA.Deletion of elements 2 and 3 caused a reduction in reporter gene expression; those constructs resulted in less than the highest level of mRNA.None of the deletions caused a reduction in reporter gene expression; all of them still resulted in reporter mRNA being made.Answer: A

154Did deletion of any of the possible control elements cause a reduction in reporter gene expression? How can you tell?Deletion of element 3 caused a reduction in reporter gene expression; that construct resulted in less than 50% of the control level of mRNA.Deletion of elements 2 and 3 caused a reduction in reporter gene expression; those constructs resulted in less than the highest level of mRNA.None of the deletions caused a reduction in reporter gene expression; all of them still resulted in reporter mRNA being made.

155If deletion of a control element causes a reduction in gene expression, what must be the normal role of that control element?To repress gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression decreases.To activate gene expression; without the control element, activators are not able to bind to the enhancer, and the level of gene expression decreases.To repress gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression increases.To activate gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression increases.Answer: B

156If deletion of a control element causes a reduction in gene expression, what must be the normal role of that control element?To repress gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression decreases.To activate gene expression; without the control element, activators are not able to bind to the enhancer, and the level of gene expression decreases.To repress gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression increases.To activate gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression increases.

157Did deletion of any of the possible control elements cause an increase in reporter gene expression? How can you tell?Deletion of control element 1 or 2 caused an increase in reporter gene expression; both constructs resulted in over 100% of the control level of mRNA.Deletion of control element 1 caused an increase in reporter gene expression; that construct resulted in the highest level of mRNA.Deletion of control element 3 caused an increase in reporter gene expression; that construct resulted in less reporter mRNA than the control.All of the deletions caused an increase in reporter gene expression; all of them still resulted in reporter mRNA being made.Answer: A

158Did deletion of any of the possible control elements cause an increase in reporter gene expression? How can you tell?Deletion of control element 1 or 2 caused an increase in reporter gene expression; both constructs resulted in over 100% of the control level of mRNA.Deletion of control element 1 caused an increase in reporter gene expression; that construct resulted in the highest level of mRNA.Deletion of control element 3 caused an increase in reporter gene expression; that construct resulted in less reporter mRNA than the control.All of the deletions caused an increase in reporter gene expression; all of them still resulted in reporter mRNA being made.

159If deletion of a control element causes an increase in gene expression, what must be the normal role of that control element?To activate gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression increases.To repress gene expression; without the control element, activators are not able to bind to the enhancer, and the level of gene expression decreases.To repress gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression increases.To activate gene expression; without the control element, activators are not able to bind to the enhancer, and the level of gene expression decreases.Answer: C

160If deletion of a control element causes an increase in gene expression, what must be the normal role of that control element?To activate gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression increases.To repress gene expression; without the control element, activators are not able to bind to the enhancer, and the level of gene expression decreases.To repress gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression increases.To activate gene expression; without the control element, activators are not able to bind to the enhancer, and the level of gene expression decreases.

161nucleic acids used to store hereditary information Which of the following is a property of life shared by prokaryotic cells and eukaryotic cells, but not viruses?nucleic acids used to store hereditary informationorder and complexity in arrangement of biological moleculesthe ability to process energy through metabolic reactionsthe capacity to evolveAnswer: C

162Which of the following is a property of life shared by prokaryotic cells and eukaryotic cells, but not viruses?nucleic acids used to store hereditary informationorder and complexity in arrangement of biological moleculesthe ability to process energy through metabolic reactionsthe capacity to evolve162

163Which of the following is characteristic of the lytic cycle?Viral DNA is incorporated into the host genome.The virus-host relationship usually lasts for generations.A large number of phages are released at a time.Many bacterial cells containing viral DNA are produced.The viral genome replicates without destroying the host.Answer: CConcept 19.2163

164Which of the following is characteristic of the lytic cycle?Viral DNA is incorporated into the host genome.The virus-host relationship usually lasts for generations.A large number of phages are released at a time.Many bacterial cells containing viral DNA are produced.The viral genome replicates without destroying the host.164

166What is the function of reverse transcriptase in retroviruses?It converts host cell RNA into viral DNA.It hydrolyzes the host cell's DNA.It uses viral RNA as a template for making complementary RNA strands.It translates viral RNA into proteins.It uses viral RNA as a template for DNA synthesis.166

167Why are viruses referred to as obligate parasites?They use the host cell to reproduce.Viral DNA always inserts itself into host DNA.They invariably kill any cell they infect.They can incorporate nucleic acids from other viruses.They must use enzymes encoded by the virus itself.Answer: A167

168Why are viruses referred to as obligate parasites?They use the host cell to reproduce.Viral DNA always inserts itself into host DNA.They invariably kill any cell they infect.They can incorporate nucleic acids from other viruses.They must use enzymes encoded by the virus itself.168

169Which of the following molecules make up the viral envelope?viral glycoproteinscapsidphospholipids from human host cell membranemembrane proteins from human host cellviral DNAAnswer: A, C, D169

170Which of the following molecules make up the viral envelope?viral glycoproteinscapsidphospholipids from human host cell membranemembrane proteins from human host cellviral DNA170

171RNA phospholipids proteins glycoproteins DNAYou have isolated viral particles from a patient, but you are not sure whether they are adenoviruses or influenza viruses. The presence of which class of biological molecules would allow you to distinguish between the two types of virus?RNAphospholipidsproteinsglycoproteinsDNAAnswer: BStudents will need to recognize that influenza viruses have an envelope, but adenoviruses do not.171

172RNA phospholipids proteins glycoproteins DNAYou have isolated viral particles from a patient, but you are not sure whether they are adenoviruses or influenza viruses. The presence of which class of biological molecules would allow you to distinguish between the two types of virus?RNAphospholipidsproteinsglycoproteinsDNA172

173The HIV virus attacks only a certain type of white blood cells, and not other cell types. Why?HIV receptors are not found on the other cell types.Reverse transcriptase cannot transcribe RNA to DNA.Viral mRNA cannot be transcribed from the integrated provirus.Viruses cannot bud from the host cell.Answer: AConcept This question examines the concept that viruses are able to recognize and attach to host cells via receptor proteins and recognition molecules on the plasma membrane.173

174The HIV virus attacks only a certain type of white blood cells, and not other cell types. Why?HIV receptors are not found on the other cell types.Reverse transcriptase cannot transcribe RNA to DNA.Viral mRNA cannot be transcribed from the integrated provirus.Viruses cannot bud from the host cell.174

175Which is not an accepted theory about the evolution of viruses:Viruses originated from naked bits of cellular nucleic acids.Genes coding for capsid proteins allowed viruses to bind cell membranes.Plasmids and transposons may have been the original sources of viral genomes.Viruses are the descendents of precellular life forms.Answer: D

176Which is not an accepted theory about the evolution of viruses:Viruses originated from naked bits of cellular nucleic acids.Genes coding for capsid proteins allowed viruses to bind cell membranes.Plasmids and transposons may have been the original sources of viral genomes.Viruses are the descendents of precellular life forms.

177AZT is a nucleoside analog used to treat HIV infectionsAZT is a nucleoside analog used to treat HIV infections. It is a modified nucleoside. Which step does AZT hamper in the reproductive cycle of the HIV virus?entry into the cellsynthesis of DNA from RNA catalyzed by reverse transcriptiontranscription of RNA from proviral DNAviral assembly within the cellAnswer: BConcept Because AZT is a thymine nucleoside, it will specifically block reverse transcription from RNA to DNA.177

178AZT is a nucleoside analog used to treat HIV infectionsAZT is a nucleoside analog used to treat HIV infections. It is a modified nucleoside. Which step does AZT hamper in the reproductive cycle of the HIV virus?entry into the cellsynthesis of DNA from RNA catalyzed by reverse transcriptiontranscription of RNA from proviral DNAviral assembly within the cell178

179Which of the following most likely describes the vertical transmission of a plant virus?The plant shows symptoms of disease after being grazed on by herbivores.Sap from one plant is rubbed on the leaves of a second plant; both plants eventually show disease symptoms.Seeds are planted and reared under protected conditions, but mature plants show disease symptoms.After a gardener prunes several plants with the same shears, they all show disease symptoms.Answer: CConcept Students will need to distinguish between horizontal transmission of disease and vertical transmission.179

180Which of the following most likely describes the vertical transmission of a plant virus?The plant shows symptoms of disease after being grazed on by herbivores.Sap from one plant is rubbed on the leaves of a second plant; both plants eventually show disease symptoms.Seeds are planted and reared under protected conditions, but mature plants show disease symptoms.After a gardener prunes several plants with the same shears, they all show disease symptoms.180

183Which is an incorrect statement about STRs (Short Tandem repeats)?They are tandemly repeated units of 5- to 10 nucleotide sequencesThe number of repeats is polymorphic from person to personTwo alleles of an STR may differ in an individualThey occur in specific regions of the genomePCR is used to amplify particular STRs.Answer: A183

184Which is an incorrect statement about STRs (Short Tandem repeats)?They are tandemly repeated units of 5- to 10 nucleotide sequencesThe number of repeats is polymorphic from person to personTwo alleles of an STR may differ in an individualThey occur in specific regions of the genomePCR is used to amplify particular STRs.184

185Which of the following beneficial traits have not resulted from DNA technology and genetic engineering of crop plants?Delayed ripeningResistance to droughtResistance to herbicidesResistance to salinitySuperweedsAnswer: E

186Which of the following beneficial traits have not resulted from DNA technology and genetic engineering of crop plants?Delayed ripeningResistance to droughtResistance to herbicidesResistance to salinitySuperweeds

187Which of the following is not a correct statement about third generation sequencing?A single DNA molecule is sequenced on its ownDifferent bases interrupt an electric current for a particular length of time a compound and an isotope; a moleculeDNA moves through a small nanopore a molecule and a compound; a moleculeDNA must be cut into fragments or amplifiedAnswer: D187

188Which of the following is not a correct statement about third generation sequencing?A single DNA molecule is sequenced on its ownDifferent bases interrupt an electric current for a particular length of time a compound and an isotope; a moleculeDNA moves through a small nanopore a molecule and a compound; a moleculeDNA must be cut into fragments or amplified188

189Place the steps in a cycle of PCR (Polymerase Chain Reaction) in the correct order:Annealing—Cool to allow primers to form hydrogen bonds with ends of target sequenceExtension—DNA polymerase adds nucleotides to the 3 end of each primerDenaturation—Heat briefly to separate DNA strands3-1-23-2-11-2-32-3-11-3-22-1-3Answer: AFigure 20.8189

190Place the steps in a cycle of PCR (Polymerase Chain Reaction) in the correct order:Annealing—Cool to allow primers to form hydrogen bonds with ends of target sequenceExtension—DNA polymerase adds nucleotides to the 3 end of each primerDenaturation—Heat briefly to separate DNA strands3-1-23-2-11-2-32-3-11-3-22-1-3190

191Which of the following is an example of “recombinant DNA”?combining alternate alleles of a gene in a single cellmanipulating a meiotic crossing-over eventcloning genes from homologous pairs of chromosomesintroducing a human gene into a bacterial plasmidalternate alleles assorting independentlyAnswer: DConcept Recombinant DNA is a DNA molecule formed when segments of DNA from two different sources—often different species—are combined in vitro (in a test tube).191

192Which of the following is an example of “recombinant DNA”?combining alternate alleles of a gene in a single cellmanipulating a meiotic crossing-over eventcloning genes from homologous pairs of chromosomesintroducing a human gene into a bacterial plasmidalternate alleles assorting independently192

193This segment of DNA is cut at restriction sites 1 and 2, which creates restriction fragments A, B, and C. Which of the following electrophoretic gels represents the separation of these fragments?a)b)c)d)Answer: ASee Figure Negative DNA moves toward the positive pole; smaller DNA fragments move faster.193

194This segment of DNA is cut at restriction sites 1 and 2, which creates restriction fragments A, B, and C. Which of the following electrophoretic gels represents the separation of these fragments?a)b)c)d)194

195Scientific Skills Exercise1) The top diagram depicts the very large regulatory region upstream of the Hoxd13 gene. The area between the slashes represents the DNA located between the promoter and the regulatory region.2) The diagrams to the left of the bar graph show, first, the intact DNA and, next, the three altered DNA sequences. A red X indicates the segment (A, B, and/or C) that was deleted in each line of transgenic mice.3) The horizontal bar graph shows the amount of Hoxd13 mRNA that was present in the digit-formation zone of each transgenic 12.5-day-old embryo paw relative to the amount that was in the digit-formation zone of a wild-type mouse that had the intact regulatory region (top bar = 100%). The paw images have blue stain visible where the Hoxd13 mRNA is located.Answer: B195

197Which of the four treatments was the control for the experiment?the wild-type mouse Cthe transgenic mouse with all three segments deleted Nthe transgenic mouse with segments B and C deletedthe transgenic mouse with only segment C deletedAnswer: A197

198Which of the four treatments was the control for the experiment?the wild-type mouse Cthe transgenic mouse with all three segments deleted Nthe transgenic mouse with segments B and C deletedthe transgenic mouse with only segment C deleted198

199The hypothesis was that all three segments of the regulatory region are required for highest expression of the Hoxd13 gene. Is this hypothesis supported by the results?Yes; when any of the segments were deleted, the expression level dropped to less than 100% of the control.No; they did not delete the promoter, so the gene could still be expressed even without the segments.Yes; when all three segments were present, the expression level was at 100%.No; even when segments were deleted, the Hoxd13 gene was still being expressed.Answer: A199

200The hypothesis was that all three segments of the regulatory region are required for highest expression of the Hoxd13 gene. Is this hypothesis supported by the results?Yes; when any of the segments were deleted, the expression level dropped to less than 100% of the control.No; they did not delete the promoter, so the gene could still be expressed even without the segments.Yes; when all three segments were present, the expression level was at 100%.No; even when segments were deleted, the Hoxd13 gene was still being expressed.200

201Only about 60% of the control amount of Hoxd13 mRNA was produced. What was the effect on the amount of Hoxd13 mRNA when segments B and C were both deleted?Only about 60% of the control amount of Hoxd13 mRNA was produced.The deletion of segments B and C had no effect on the amount of Hoxd13 mRNA produced.Only about 35% of the control amount of Hoxd13 mRNA was produced.Only about 5% of the control amount of Hoxd13 mRNA was produced.Answer: C201

202Only about 60% of the control amount of Hoxd13 mRNA was produced. What was the effect on the amount of Hoxd13 mRNA when segments B and C were both deleted?Only about 60% of the control amount of Hoxd13 mRNA was produced.The deletion of segments B and C had no effect on the amount of Hoxd13 mRNA produced.Only about 35% of the control amount of Hoxd13 mRNA was produced.Only about 5% of the control amount of Hoxd13 mRNA was produced.202

203Look at the blue stain in the in situ hybridization for the transgenic mouse lacking segments B and C. How would you describe the spatial pattern of gene expression in the embryo paw as compared to the control?There is very light blue stain in the center of each digit zone as compared to the control.The blue stain is generally lighter than in the control, but all four digit zones are still visible.There is almost no blue stain anywhere in the paw as compared to the control.There is no blue stain at the base of the paw as compared to the control.Answer: B203

205Look at the blue stain in the in situ hybridization for the transgenic mouse lacking segments B and C. How would you describe the spatial pattern of gene expression in the embryo paw as compared to the control?There is very light blue stain in the center of each digit zone as compared to the control.The blue stain is generally lighter than in the control, but all four digit zones are still visible.There is almost no blue stain anywhere in the paw as compared to the control.There is no blue stain at the base of the paw as compared to the control.205

206Only about 60% of the control amount of Hoxd13 mRNA was produced. What was the effect on the amount of Hoxd13 mRNA when just segment C was deleted?The deletion of segment C had no effect on the amount of Hoxd13 mRNA produced.Only about 60% of the control amount of Hoxd13 mRNA was produced.Only about 35% of the control amount of Hoxd13 mRNA was produced.Only about 5% of the control amount of Hoxd13 mRNA was produced.Answer: B206

207Only about 60% of the control amount of Hoxd13 mRNA was produced. What was the effect on the amount of Hoxd13 mRNA when just segment C was deleted?The deletion of segment C had no effect on the amount of Hoxd13 mRNA produced.Only about 60% of the control amount of Hoxd13 mRNA was produced.Only about 35% of the control amount of Hoxd13 mRNA was produced.Only about 5% of the control amount of Hoxd13 mRNA was produced.207

208How would you describe the spatial pattern of gene expression in the embryo paw lacking segment C as compared to the control and to the paw lacking segments B and C?The digit zones are not visibly stained as they are in the control and the paw lacking B and C.The top of the paw is stained darker than both the control and the paw lacking B and C.The base of the paw is stained darker than both the control and the paw lacking B and C.The digit zones are defined with darker stain than both the control and the paw lacking B and C.Answer: A208

209How would you describe the spatial pattern of gene expression in the embryo paw lacking segment C as compared to the control and to the paw lacking segments B and C?The digit zones are not visibly stained as they are in the control and the paw lacking B and C.The top of the paw is stained darker than both the control and the paw lacking B and C.The base of the paw is stained darker than both the control and the paw lacking B and C.The digit zones are defined with darker stain than both the control and the paw lacking B and C.209

210Suppose the researchers had only measured the amount of Hoxd13 mRNA and not done the in situ hybridizations. What important information about the role of the regulatory segments would have been missed?The interaction of the regulatory region with the promoter would have been missed.The interaction among the different segments of the regulatory region would have been missed.The mRNA would not have been blue; therefore it could not have been measured for the results shown in the bar graph.The spatial patterns of Hoxd13 gene expression in the paws would have been missed.Answer: D210

211Suppose the researchers had only measured the amount of Hoxd13 mRNA and not done the in situ hybridizations. What important information about the role of the regulatory segments would have been missed?The interaction of the regulatory region with the promoter would have been missed.The interaction among the different segments of the regulatory region would have been missed.The mRNA would not have been blue; therefore it could not have been measured for the results shown in the bar graph.The spatial patterns of Hoxd13 gene expression in the paws would have been missed.211

212Qualitative data about Hoxd13 mRNA levels would have been missed. Suppose the researchers had only done the in situ hybridizations and not measured the amount of Hoxd13 mRNA. What important information would have been missed?The information about which regulatory segments were deleted would have been missed.The spatial patterns of Hoxd13 gene expression in the paws would have been missed.Qualitative data about Hoxd13 mRNA levels would have been missed.Quantitative data about Hoxd13 mRNA levels would have been missed.Answer: D212

213Qualitative data about Hoxd13 mRNA levels would have been missed. Suppose the researchers had only done the in situ hybridizations and not measured the amount of Hoxd13 mRNA. What important information would have been missed?The information about which regulatory segments were deleted would have been missed.The spatial patterns of Hoxd13 gene expression in the paws would have been missed.Qualitative data about Hoxd13 mRNA levels would have been missed.Quantitative data about Hoxd13 mRNA levels would have been missed.213